pyobo 0.10.10__py3-none-any.whl → 0.10.12__py3-none-any.whl

pyobo/sources/antibodyregistry.py

@@ -5,12 +5,12 @@
 import logging
 from typing import Iterable, Mapping, Optional
 
-import bioversions
 import pandas as pd
 from bioregistry.utils import removeprefix
 from tqdm.auto import tqdm
 
 from pyobo import Obo, Term
+from pyobo.api.utils import get_version
 from pyobo.utils.path import ensure_df
 
 __all__ = [
@@ -24,9 +24,10 @@ URL = "http://antibodyregistry.org/php/fileHandler.php"
 CHUNKSIZE = 20_000
 
 
-def get_chunks(force: bool = False) -> pd.DataFrame:
+def get_chunks(*, force: bool = False, version: Optional[str] = None) -> pd.DataFrame:
     """Get the BioGRID identifiers mapping dataframe."""
-    version = bioversions.get_version(PREFIX)
+    if version is None:
+        version = get_version(PREFIX)
     df = ensure_df(
         PREFIX,
         url=URL,
@@ -47,7 +48,7 @@ class AntibodyRegistryGetter(Obo):
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return iter_terms(force=force)
+        return iter_terms(force=force, version=self._version_or_raise)
 
 
 def get_obo(*, force: bool = False) -> Obo:
@@ -74,9 +75,9 @@ SKIP = {
 }
 
 
-def iter_terms(force: bool = False) -> Iterable[Term]:
+def iter_terms(*, force: bool = False, version: Optional[str] = None) -> Iterable[Term]:
     """Iterate over antibodies."""
-    chunks = get_chunks(force=force)
+    chunks = get_chunks(force=force, version=version)
     needs_curating = set()
     # df['vendor'] = df['vendor'].map(bioregistry.normalize_prefix)
     it = tqdm(chunks, desc=f"{PREFIX}, chunkssize={CHUNKSIZE}")

pyobo/sources/biogrid.py

@@ -2,12 +2,12 @@
 
 """Extract and convert BioGRID identifiers."""
 
+from functools import partial
 from typing import Mapping, Optional
 
-import bioversions
 import pandas as pd
 
-from pyobo.constants import version_getter
+from pyobo.api.utils import get_version
 from pyobo.resources.ncbitaxon import get_ncbitaxon_id
 from pyobo.utils.cache import cached_mapping
 from pyobo.utils.path import ensure_df, prefix_directory_join
@@ -52,7 +52,7 @@ def _lookup(name: str) -> Optional[str]:
 
 def get_df() -> pd.DataFrame:
     """Get the BioGRID identifiers mapping dataframe."""
-    version = bioversions.get_version("biogrid")
+    version = get_version("biogrid")
     url = f"{BASE_URL}/BIOGRID-{version}/BIOGRID-IDENTIFIERS-{version}.tab.zip"
     df = ensure_df(PREFIX, url=url, skiprows=28, dtype=str, version=version)
     df["taxonomy_id"] = df["ORGANISM_OFFICIAL_NAME"].map(_lookup)
@@ -61,7 +61,11 @@ def get_df() -> pd.DataFrame:
 
 @cached_mapping(
     path=prefix_directory_join(
-        PREFIX, "cache", "xrefs", name="ncbigene.tsv", version=version_getter(PREFIX)
+        PREFIX,
+        "cache",
+        "xrefs",
+        name="ncbigene.tsv",
+        version=partial(get_version, PREFIX),
     ),
     header=["biogrid_id", "ncbigene_id"],
 )

pyobo/sources/ccle.py

@@ -50,7 +50,7 @@ def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[T
         yield term
 
 
-def get_version() -> str:
+def get_ccle_static_version() -> str:
     """Get the default version of CCLE's cell lines."""
     return "2019"
 
@@ -58,21 +58,21 @@ def get_version() -> str:
 def get_url(version: Optional[str] = None) -> str:
     """Get the cBioPortal URL for the given version of CCLE's cell lines."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     return f"https://cbioportal-datahub.s3.amazonaws.com/ccle_broad_{version}.tar.gz"
 
 
 def get_inner(version: Optional[str] = None) -> str:
     """Get the inner tarfile path."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     return f"ccle_broad_{version}/data_clinical_sample.txt"
 
 
 def ensure(version: Optional[str] = None, **kwargs) -> Path:
     """Ensure the given version is downloaded."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     url = get_url(version=version)
     return pystow.ensure("pyobo", "raw", PREFIX, version, url=url, **kwargs)
 
@@ -80,7 +80,7 @@ def ensure(version: Optional[str] = None, **kwargs) -> Path:
 def ensure_df(version: Optional[str] = None, force: bool = False) -> pd.DataFrame:
     """Get the CCLE clinical sample dataframe."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     path = ensure(version=version, force=force)
     inner_path = get_inner(version=version)
     with tarfile.open(path) as tf:

pyobo/sources/credit.py

@@ -0,0 +1,68 @@
+"""Converter for the Contributor Roles Taxonomy."""
+
+from __future__ import annotations
+
+import json
+from typing import Iterable
+
+from more_itertools import chunked
+
+from pyobo.struct import Obo, Term
+from pyobo.utils.path import ensure_path
+
+__all__ = [
+    "CreditGetter",
+]
+
+url = "https://api.github.com/repos/CASRAI-CRedIT/Dictionary/contents/Picklists/Contributor%20Roles"
+PREFIX = "credit"
+
+
+class CreditGetter(Obo):
+    """An ontology representation of the Contributor Roles Taxonomy."""
+
+    ontology = PREFIX
+    static_version = "2022"
+    idspaces = {
+        PREFIX: "https://credit.niso.org/contributor-roles/",
+    }
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return get_terms(force=force)
+
+
+def get_obo(force: bool = False) -> Obo:
+    """Get RGD as OBO."""
+    return CreditGetter(force=force)
+
+
+def get_terms(force: bool = False) -> list[Term]:
+    """Get terms from the Contributor Roles Taxonomy via GitHub."""
+    path = ensure_path(PREFIX, url=url, name="picklist-api.json", force=force)
+    with open(path) as f:
+        data = json.load(f)
+    terms = []
+    for x in data:
+        name = x["name"].removesuffix(".md").lower()
+
+        pp = ensure_path(PREFIX, "picklist", url=x["download_url"], backend="requests")
+        with open(pp) as f:
+            header, *rest = f.read().splitlines()
+            name = header = header.removeprefix("# Contributor Roles/")
+            dd = {k.removeprefix("## "): v for k, v in chunked(rest, 2)}
+            identifier = (
+                dd["Canonical URL"]
+                .removeprefix("https://credit.niso.org/contributor-roles/")
+                .rstrip("/")
+            )
+            desc = dd["Short definition"]
+            terms.append(
+                Term.from_triple(prefix=PREFIX, identifier=identifier, name=name, definition=desc)
+            )
+
+    return terms
+
+
+if __name__ == "__main__":
+    get_obo(force=True).write_default(write_obo=True)

pyobo/sources/geonames.py

@@ -1,5 +1,7 @@
 """Get terms from geonames."""
 
+from __future__ import annotations
+
 import logging
 from typing import Collection, Iterable, Mapping
 
@@ -146,15 +148,7 @@ def get_code_to_admin2(
     return code_to_admin2
 
 
-def get_cities(
-    code_to_country,
-    code_to_admin1,
-    code_to_admin2,
-    *,
-    minimum_population: int = 100_000,
-    force: bool = False,
-) -> Mapping[str, Term]:
-    """Get a mapping from city code to term."""
+def _get_cities_df(force: bool = False) -> pd.DataFrame:
     columns = [
         "geonames_id",
         "name",
@@ -184,7 +178,19 @@ def get_cities(
         names=columns,
         dtype=str,
     )
+    return cities_df
+
 
+def get_cities(
+    code_to_country,
+    code_to_admin1,
+    code_to_admin2,
+    *,
+    minimum_population: int = 100_000,
+    force: bool = False,
+) -> Mapping[str, Term]:
+    """Get a mapping from city code to term."""
+    cities_df = _get_cities_df(force=force)
     cities_df = cities_df[cities_df.population.astype(int) > minimum_population]
     cities_df.synonyms = cities_df.synonyms.str.split(",")
 
@@ -235,5 +241,17 @@ def get_cities(
     return terms
 
 
+def get_city_to_country() -> dict[str, str]:
+    """Get a mapping from city GeoNames to country GeoNames id."""
+    rv = {}
+    code_to_country = get_code_to_country()
+    cities_df = _get_cities_df()
+    for city_geonames_id, country_code in cities_df[["geonames_id", "country_code"]].values:
+        if pd.isna(city_geonames_id) or pd.isna(country_code):
+            continue
+        rv[city_geonames_id] = code_to_country[country_code].identifier
+    return rv
+
+
 if __name__ == "__main__":
     GeonamesGetter().write_default(write_obo=True, force=True)

pyobo/sources/hgnc.py

@@ -10,10 +10,10 @@ from collections import Counter, defaultdict
 from operator import attrgetter
 from typing import DefaultDict, Dict, Iterable, Optional
 
-import bioversions
 from tabulate import tabulate
 from tqdm.auto import tqdm
 
+from pyobo.api.utils import get_version
 from pyobo.struct import (
     Obo,
     Reference,
@@ -241,7 +241,7 @@ def get_obo(*, force: bool = False) -> Obo:
 def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:  # noqa:C901
     """Get HGNC terms."""
     if version is None:
-        version = bioversions.get_version("hgnc")
+        version = get_version("hgnc")
     unhandled_entry_keys: typing.Counter[str] = Counter()
     unhandle_locus_types: DefaultDict[str, Dict[str, Term]] = defaultdict(dict)
     path = ensure_path(

pyobo/sources/mesh.py

@@ -11,6 +11,7 @@ from xml.etree.ElementTree import Element
 
 from tqdm.auto import tqdm
 
+from pyobo.api.utils import get_version
 from pyobo.identifier_utils import standardize_ec
 from pyobo.struct import Obo, Reference, Synonym, Term
 from pyobo.utils.cache import cached_json, cached_mapping
@@ -318,21 +319,22 @@ def _get_descriptor_qualifiers(descriptor: Element) -> List[Mapping[str, str]]:
     ]
 
 
-def get_mesh_category_curies(letter: str, skip: Optional[Collection[str]] = None) -> List[str]:
+def get_mesh_category_curies(
+    letter: str, *, skip: Optional[Collection[str]] = None, version: Optional[str] = None
+) -> List[str]:
     """Get the MeSH LUIDs for a category, by letter (e.g., "A").
 
     :param letter: The MeSH tree, A for anatomy, C for disease, etc.
     :param skip: An optional collection of MeSH tree codes to skip, such as "A03"
+    :param version: The MeSH version to use. Defaults to latest
     :returns: A list of MeSH CURIE strings for the top level of each MeSH tree.
 
     .. seealso:: https://meshb.nlm.nih.gov/treeView
     """
-    import bioversions
-
-    mesh_version = bioversions.get_version("mesh")
-    if mesh_version is None:
-        raise ValueError
-    tree_to_mesh = get_tree_to_mesh_id(mesh_version)
+    if version is None:
+        version = get_version("mesh")
+        assert version is not None
+    tree_to_mesh = get_tree_to_mesh_id(version=version)
     rv = []
     for i in range(1, 100):
         key = f"{letter}{i:02}"

pyobo/sources/msigdb.py

@@ -137,7 +137,7 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
 def _get_definition(attrib) -> Optional[str]:
     rv = attrib["DESCRIPTION_FULL"].strip() or attrib["DESCRIPTION_BRIEF"].strip() or None
     if rv is not None:
-        return rv.replace("\d", "").replace("\s", "")  # noqa: W605
+        return rv.replace(r"\d", "").replace(r"\s", "")  # noqa: W605
     return None
 
 

pyobo/sources/npass.py

@@ -64,7 +64,7 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
         )
 
         for xref_prefix, xref_id in [
-            ("chembl", chembl_id),
+            ("chembl.compound", chembl_id),
             # ("zinc", zinc_id),
         ]:
             if pd.notna(xref_id):

pyobo/sources/pubchem.py

@@ -5,12 +5,12 @@
 import logging
 from typing import Iterable, Mapping, Optional
 
-import bioversions
 import pandas as pd
 from bioregistry.utils import removeprefix
 from tqdm.auto import tqdm
 
 from ..api import get_name_id_mapping
+from ..api.utils import get_version
 from ..struct import Obo, Reference, Synonym, Term
 from ..utils.iter import iterate_gzips_together
 from ..utils.path import ensure_df, ensure_path
@@ -26,7 +26,7 @@ PREFIX = "pubchem.compound"
 
 def _get_pubchem_extras_url(version: Optional[str], end: str) -> str:
     if version is None:
-        version = bioversions.get_version("pubchem")
+        version = get_version("pubchem")
     return f"ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/{version}/Extras/{end}"
 
 
@@ -100,7 +100,7 @@ def get_pubchem_id_to_mesh_id(version: str) -> Mapping[str, str]:
 
 def _ensure_cid_name_path(*, version: Optional[str] = None, force: bool = False) -> str:
     if version is None:
-        version = bioversions.get_version("pubchem")
+        version = get_version("pubchem")
     # 2 tab-separated columns: compound_id, name
     cid_name_url = _get_pubchem_extras_url(version, "CID-Title.gz")
     cid_name_path = ensure_path(PREFIX, url=cid_name_url, version=version, force=force)

pyobo/sources/rgd.py

@@ -28,7 +28,7 @@ old_name_type = SynonymTypeDef.from_text("old_name")
 
 # NOTE unigene id was discontinue in January 18th, 2021 dump
 
-GENES_URL = "https://download.rgd.mcw.edu/data_release/GENES.RAT.txt"
+GENES_URL = "https://download.rgd.mcw.edu/data_release/GENES_RAT.txt"
 GENES_HEADER = [
     "GENE_RGD_ID",
     "SYMBOL",

pyobo/sources/rhea.py

@@ -5,9 +5,9 @@
 import logging
 from typing import TYPE_CHECKING, Dict, Iterable, Optional
 
-import bioversions
 import pystow
 
+from pyobo.api.utils import get_version
 from pyobo.struct import Obo, Reference, Term
 from pyobo.struct.typedef import (
     TypeDef,
@@ -63,7 +63,7 @@ def ensure_rhea_rdf(version: Optional[str] = None, force: bool = False) -> "rdfl
     """Get the Rhea RDF graph."""
     # see docs: https://ftp.expasy.org/databases/rhea/rdf/rhea_rdf_documentation.pdf
     if version is None:
-        version = bioversions.get_version(PREFIX)
+        version = get_version(PREFIX)
     return pystow.ensure_rdf(
         "pyobo",
         "raw",

pyobo/sources/ror.py

@@ -1,34 +1,40 @@
 """Convert the Research Organization Registry (ROR) into an ontology."""
 
+from __future__ import annotations
+
 import json
 import zipfile
-from typing import Iterable
+from typing import Any, Iterable
 
 import bioregistry
 import zenodo_client
 from tqdm.auto import tqdm
 
-from pyobo.struct import Obo, Reference, Term, TypeDef
+from pyobo.struct import Obo, Reference, Term
 from pyobo.struct.struct import acronym
+from pyobo.struct.typedef import (
+    has_homepage,
+    has_part,
+    has_predecessor,
+    has_successor,
+    located_in,
+    part_of,
+    see_also,
+)
 
 PREFIX = "ror"
 ROR_ZENODO_RECORD_ID = "10086202"
 
 # Constants
 ORG_CLASS = Reference(prefix="OBI", identifier="0000245")
-LOCATED_IN = Reference(prefix="RO", identifier="0001025")
-PART_OF = Reference(prefix="BFO", identifier="0000050")
-HAS_PART = Reference(prefix="BFO", identifier="0000051")
-SUCCESSOR = Reference(prefix="BFO", identifier="0000063")
-PREDECESSOR = Reference(prefix="BFO", identifier="0000062")
 
 RMAP = {
-    "Related": TypeDef.from_triple("rdfs", "seeAlso"),
-    "Child": TypeDef(HAS_PART),
-    "Parent": TypeDef(PART_OF),
-    "Predecessor": TypeDef(PREDECESSOR),
-    "Successor": TypeDef(SUCCESSOR),
-    "Located in": TypeDef(LOCATED_IN),
+    "Related": see_also,
+    "Child": has_part,
+    "Parent": part_of,
+    "Predecessor": has_predecessor,
+    "Successor": has_successor,
+    "Located in": located_in,
 }
 NAME_REMAPPING = {
     "'s-Hertogenbosch": "Den Bosch",  # SMH Netherlands, why u gotta be like this
@@ -43,16 +49,16 @@ class RORGetter(Obo):
     """An ontology representation of the ROR."""
 
     ontology = bioregistry_key = PREFIX
-    typedefs = list(RMAP.values())
+    typedefs = [has_homepage, *RMAP.values()]
     synonym_typedefs = [acronym]
     idspaces = {
         "ror": "https://ror.org/",
         "geonames": "https://www.geonames.org/",
-        "envo": "http://purl.obolibrary.org/obo/ENVO_",
-        "bfo": "http://purl.obolibrary.org/obo/BFO_",
-        "ro": "http://purl.obolibrary.org/obo/RO_",
-        "obi": "http://purl.obolibrary.org/obo/OBI_",
-        "omo": "http://purl.obolibrary.org/obo/OMO_",
+        "ENVO": "http://purl.obolibrary.org/obo/ENVO_",
+        "BFO": "http://purl.obolibrary.org/obo/BFO_",
+        "RO": "http://purl.obolibrary.org/obo/RO_",
+        "OBI": "http://purl.obolibrary.org/obo/OBI_",
+        "OMO": "http://purl.obolibrary.org/obo/OMO_",
         "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
     }
 
@@ -65,6 +71,18 @@ class RORGetter(Obo):
         return iterate_ror_terms(force=force)
 
 
+ROR_ORGANIZATION_TYPE_TO_OBI = {
+    "Education": ...,
+    "Facility": ...,
+    "Company": ...,
+    "Government": ...,
+    "Healthcare": ...,
+    "Other": ...,
+    "Archive": ...,
+}
+_MISSED_ORG_TYPES: set[str] = set()
+
+
 def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
     """Iterate over terms in ROR."""
     version, source_uri, records = get_latest(force=force)
@@ -74,10 +92,23 @@ def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
         name = record["name"]
         name = NAME_REMAPPING.get(name, name)
 
+        organization_types = record.get("types", [])
+        description = f"{organization_types[0]} in {record['country']['country_name']}"
+        if established := record["established"]:
+            description += f" established in {established}"
+
         term = Term(
-            reference=Reference(prefix=PREFIX, identifier=identifier, name=name), type="Instance"
+            reference=Reference(prefix=PREFIX, identifier=identifier, name=name),
+            type="Instance",
+            definition=description,
         )
         term.append_parent(ORG_CLASS)
+        # TODO replace term.append_parent(ORG_CLASS) with:
+        # for organization_type in organization_types:
+        #     term.append_parent(ORG_PARENTS[organization_type])
+
+        for link in record.get("links", []):
+            term.append_property(has_homepage, link)
 
         if name.startswith("The "):
             term.append_synonym(name.removeprefix("The "))
@@ -159,5 +190,20 @@ def get_latest(*, force: bool = False):
     raise FileNotFoundError
 
 
+def get_ror_to_country_geonames(**kwargs: Any) -> dict[str, str]:
+    """Get a mapping of ROR ids to GeoNames IDs for countries."""
+    from pyobo.sources.geonames import get_city_to_country
+
+    city_to_country = get_city_to_country()
+    rv = {}
+    for term in iterate_ror_terms(**kwargs):
+        city_geonames_reference = term.get_relationship(located_in)
+        if city_geonames_reference is None:
+            continue
+        if city_geonames_reference.identifier in city_to_country:
+            rv[term.identifier] = city_to_country[city_geonames_reference.identifier]
+    return rv
+
+
 if __name__ == "__main__":
-    RORGetter().write_default(write_obo=True, force=True)
+    RORGetter(force=True).write_default(write_obo=True, force=True)

pyobo/sources/uniprot/uniprot.py

@@ -6,10 +6,10 @@ from operator import attrgetter
 from pathlib import Path
 from typing import Iterable, List, Optional, cast
 
-import bioversions
 from tqdm.auto import tqdm
 
 from pyobo import Obo, Reference
+from pyobo.api.utils import get_version
 from pyobo.constants import RAW_MODULE
 from pyobo.identifier_utils import standardize_ec
 from pyobo.struct import Term, derives_from, enables, from_species, participates_in
@@ -166,7 +166,7 @@ def _parse_go(go_terms) -> List[Reference]:
 def ensure(version: Optional[str] = None, force: bool = False) -> Path:
     """Ensure the reviewed uniprot names are available."""
     if version is None:
-        version = bioversions.get_version("uniprot")
+        version = get_version("uniprot")
     return RAW_MODULE.ensure(
         PREFIX,
         version,

pyobo/struct/struct.py

@@ -56,6 +56,7 @@ from .typedef import (
     term_replaced_by,
 )
 from .utils import comma_separate, obo_escape_slim
+from ..api.utils import get_version
 from ..constants import (
     DATE_FORMAT,
     NCBITAXON_PREFIX,
@@ -77,6 +78,8 @@ __all__ = [
     "Term",
     "Obo",
     "make_ad_hoc_ontology",
+    "abbreviation",
+    "acronym",
 ]
 
 logger = logging.getLogger(__name__)
@@ -583,10 +586,8 @@ class Obo:
 
     def _get_version(self) -> Optional[str]:
         if self.bioversions_key:
-            import bioversions
-
             try:
-                return bioversions.get_version(self.bioversions_key)
+                return get_version(self.bioversions_key)
             except KeyError:
                 logger.warning(f"[{self.bioversions_key}] bioversions doesn't list this resource ")
             except IOError:

pyobo/struct/typedef.py

@@ -42,9 +42,13 @@ __all__ = [
     "has_participant",
     "exact_match",
     "has_dbxref",
+    "located_in",
+    "has_successor",
+    "has_predecessor",
     # Properties
     "has_inchi",
     "has_smiles",
+    "has_homepage",
 ]
 
 
@@ -323,6 +327,9 @@ enabled_by = TypeDef(reference=_enabled_by_reference, inverse=_enables_reference
 has_input = TypeDef.from_triple(prefix=RO_PREFIX, identifier="0002233", name="has input")
 has_output = TypeDef.from_triple(prefix=RO_PREFIX, identifier="0002234", name="has output")
 
+has_successor = TypeDef.from_triple(prefix="BFO", identifier="0000063", name="has successor")
+has_predecessor = TypeDef.from_triple(prefix="BFO", identifier="0000062", name="has predecessor")
+
 """ChEBI"""
 
 is_conjugate_base_of = TypeDef(
@@ -355,6 +362,9 @@ has_inchi = TypeDef(
     reference=Reference(prefix="debio", identifier="0000020", name="has InChI"),
 )
 
+has_homepage = TypeDef(
+    reference=Reference(prefix="foaf", identifier="homepage", name="homepage"), is_metadata_tag=True
+)
 
 default_typedefs: Dict[Tuple[str, str], TypeDef] = {
     v.pair: v for k, v in locals().items() if isinstance(v, TypeDef)

pyobo/utils/path.py

@@ -25,7 +25,7 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 
-VersionHint = Union[None, str, Callable[[], str]]
+VersionHint = Union[None, str, Callable[[], Optional[str]]]
 
 requests_ftp.monkeypatch_session()
 
@@ -46,6 +46,7 @@ def prefix_directory_join(
         logger.info("[%s] got version %s", prefix, version)
     elif not isinstance(version, str):
         raise TypeError(f"Invalid type: {version} ({type(version)})")
+    assert version is not None
     version = cleanup_version(version, prefix=prefix)
     if version is not None and "/" in version:
         raise ValueError(f"[{prefix}] Can not have slash in version: {version}")

pyobo/version.py

@@ -14,7 +14,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.10.10"
+VERSION = "0.10.12"
 
 
 def get_git_hash() -> str: